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- Reconcile docs and code for max_twa_parent
- Correct links to docs in twa vignette
- Static documentation rebuilt by pkgdown

1 files changed, 27 insertions, 22 deletions

diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
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@@ -7,8 +7,9 @@
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 <title>Performance benefit by using compiled model definitions in mkin • mkin</title>
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       <h1>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-07-09</h4>
+            <h4 class="date">2019-09-18</h4>
       
       
       <div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -101,18 +103,18 @@
 <h2 class="hasAnchor">
 <a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"></a>Model that can also be solved with Eigenvalues</h2>
 <p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Sys.which">Sys.which</a></span>(<span class="st">"gcc"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/Sys.which.html">Sys.which</a></span>(<span class="st">"gcc"</span>)</a></code></pre></div>
 <pre><code>##            gcc 
 ## "/usr/bin/gcc"</code></pre>
 <p>First, we build a simple degradation model for a parent compound with one metabolite.</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
 <a class="sourceLine" id="cb3-2" title="2">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
 <a class="sourceLine" id="cb3-3" title="3">  <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a>
 <a class="sourceLine" id="cb3-4" title="4">  <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
 <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a>
-<a class="sourceLine" id="cb5-2" title="2">  b<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span>(rbenchmark)) {</a>
+<a class="sourceLine" id="cb5-2" title="2">  b<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span>(</a>
 <a class="sourceLine" id="cb5-3" title="3">    <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a>
 <a class="sourceLine" id="cb5-4" title="4">                                      <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,</a>
 <a class="sourceLine" id="cb5-5" title="5">                                      <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
@@ -121,11 +123,11 @@
 <a class="sourceLine" id="cb5-8" title="8">    <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a>
 <a class="sourceLine" id="cb5-9" title="9">                                  <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
 <a class="sourceLine" id="cb5-10" title="10">    <span class="dt">replications =</span> <span class="dv">3</span>)</a>
-<a class="sourceLine" id="cb5-11" title="11">  <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.1</span>)</a>
-<a class="sourceLine" id="cb5-12" title="12">  factor_SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a>
+<a class="sourceLine" id="cb5-11" title="11">  <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(b<span class="fl">.1</span>)</a>
+<a class="sourceLine" id="cb5-12" title="12">  factor_SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/Round.html">round</a></span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a>
 <a class="sourceLine" id="cb5-13" title="13">} <span class="cf">else</span> {</a>
 <a class="sourceLine" id="cb5-14" title="14">  factor_SFO_SFO &lt;-<span class="st"> </span><span class="ot">NA</span></a>
-<a class="sourceLine" id="cb5-15" title="15">  <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>)</a>
+<a class="sourceLine" id="cb5-15" title="15">  <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>)</a>
 <a class="sourceLine" id="cb5-16" title="16">}</a></code></pre></div>
 <pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
 <pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
@@ -163,9 +165,9 @@
 ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
 ## = TRUE): Observations with value of zero were removed from the data</code></pre>
 <pre><code>##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.127    1.000     3.125        0
-## 1 deSolve, not compiled            3  28.337    9.062    28.322        0
-## 2      Eigenvalue based            3   4.320    1.382     4.317        0
+## 3     deSolve, compiled            3   3.124    1.000     3.122        0
+## 1 deSolve, not compiled            3  28.822    9.226    28.807        0
+## 2      Eigenvalue based            3   4.416    1.414     4.413        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -176,21 +178,21 @@
 <h2 class="hasAnchor">
 <a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>Model that can not be solved with Eigenvalues</h2>
 <p>This evaluation is also taken from the example section of mkinfit.</p>
-<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a>
+<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://rdrr.io/r/base/library.html">require</a></span>(rbenchmark)) {</a>
 <a class="sourceLine" id="cb14-2" title="2">  FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
 <a class="sourceLine" id="cb14-3" title="3">    <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a>
 <a class="sourceLine" id="cb14-4" title="4">    <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a>
 <a class="sourceLine" id="cb14-5" title="5"></a>
-<a class="sourceLine" id="cb14-6" title="6">  b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a>
+<a class="sourceLine" id="cb14-6" title="6">  b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span>(</a>
 <a class="sourceLine" id="cb14-7" title="7">    <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,</a>
 <a class="sourceLine" id="cb14-8" title="8">                                      <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
 <a class="sourceLine" id="cb14-9" title="9">    <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
 <a class="sourceLine" id="cb14-10" title="10">    <span class="dt">replications =</span> <span class="dv">3</span>)</a>
-<a class="sourceLine" id="cb14-11" title="11">  <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.2</span>)</a>
-<a class="sourceLine" id="cb14-12" title="12">  factor_FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a>
+<a class="sourceLine" id="cb14-11" title="11">  <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(b<span class="fl">.2</span>)</a>
+<a class="sourceLine" id="cb14-12" title="12">  factor_FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/Round.html">round</a></span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a>
 <a class="sourceLine" id="cb14-13" title="13">} <span class="cf">else</span> {</a>
 <a class="sourceLine" id="cb14-14" title="14">  factor_FOMC_SFO &lt;-<span class="st"> </span><span class="ot">NA</span></a>
-<a class="sourceLine" id="cb14-15" title="15">  <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a>
+<a class="sourceLine" id="cb14-15" title="15">  <span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a>
 <a class="sourceLine" id="cb14-16" title="16">}</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
 <pre><code>## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
@@ -214,14 +216,14 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data</code></pre>
 <pre><code>##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.783    1.000     4.780        0
-## 1 deSolve, not compiled            3  52.761   11.031    52.733        0
+## 2     deSolve, compiled            3   4.878    1.000     4.875        0
+## 1 deSolve, not compiled            3  53.602   10.989    53.568        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0</code></pre>
 <p>Here we get a performance benefit of a factor of 11 using the version of the differential equation model compiled from C code!</p>
 <p>This vignette was built with mkin 0.9.49.6 on</p>
-<pre><code>## R version 3.6.0 (2019-04-26)
+<pre><code>## R version 3.6.1 (2019-07-05)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 10 (buster)</code></pre>
 <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre>
@@ -242,17 +244,20 @@
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